Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D05
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 63323194
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1953226 characters in sequence are not A, C, G, or T
File 175 of 199
Found at i:56269668 original size:16 final size:16
Alignment explanation
Indices: 56269661--56269728 Score: 118
Period size: 16 Copynumber: 4.2 Consensus size: 16
56269651 TTATGTGTGT
*
56269661 TGTAAGTTGTAAGTTA
1 TGTAAGTTATAAGTTA
56269677 TGTAAGTTATAAGTTA
1 TGTAAGTTATAAGTTA
56269693 TGTAAGTTATAAGTTA
1 TGTAAGTTATAAGTTA
*
56269709 TGTAAGTTGTAAGTTA
1 TGTAAGTTATAAGTTA
56269725 TGTA
1 TGTA
56269729 TAATATTAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.22, T:0.44
Consensus pattern (16 bp):
TGTAAGTTATAAGTTA
Found at i:56269671 original size:7 final size:7
Alignment explanation
Indices: 56269659--56269723 Score: 58
Period size: 7 Copynumber: 8.4 Consensus size: 7
56269649 AGTTATGTGT
56269659 GTTGTAA
1 GTTGTAA
56269666 GTTGTAA
1 GTTGTAA
56269673 GTTATGTAA
1 G-T-TGTAA
*
56269682 GTTATAA
1 GTTGTAA
56269689 GTTATGTAA
1 G-T-TGTAA
*
56269698 GTTATAA
1 GTTGTAA
56269705 GTTATGTAA
1 G-T-TGTAA
56269714 GTTGTAA
1 GTTGTAA
56269721 GTT
1 GTT
56269724 ATGTATAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
7 26 0.54
8 6 0.12
9 16 0.33
ACGTcount: A:0.32, C:0.00, G:0.23, T:0.45
Consensus pattern (7 bp):
GTTGTAA
Found at i:56269675 original size:23 final size:23
Alignment explanation
Indices: 56269647--56269727 Score: 83
Period size: 23 Copynumber: 3.4 Consensus size: 23
56269637 ATTAACTAAT
56269647 TAAGTTATGTGTGTTGTAAGTTG
1 TAAGTTATGTGTGTTGTAAGTTG
** *
56269670 TAAGTTATGTAAGTTATAAGTTATG
1 TAAGTTATGTGTGTTGTAAG-T-TG
**
56269695 TAAGTTATAAGT-TATGTAAGTTG
1 TAAGTTATGTGTGT-TGTAAGTTG
56269718 TAAGTTATGT
1 TAAGTTATGT
56269728 ATAATATTAA
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
23 27 0.60
24 3 0.07
25 15 0.33
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (23 bp):
TAAGTTATGTGTGTTGTAAGTTG
Found at i:56269747 original size:48 final size:47
Alignment explanation
Indices: 56269623--56269750 Score: 120
Period size: 48 Copynumber: 2.7 Consensus size: 47
56269613 AACTAAGTTA
* * * **
56269623 TGTAATTTATGT--ATATTAACTAATTAAGTTATGTGTGTTGTAAGT
1 TGTAAGTTATGTAAATATTAATTAACTAAGTTATAAGTGTTGTAAGT
* **
56269668 TGTAAGTTATGTAAGT-TATAAGTTATGTAAGTTATAAGT-TATGTAAGT
1 TGTAAGTTATGTAAATAT-TAA-TTAACTAAGTTATAAGTGT-TGTAAGT
56269716 TGTAAGTTATGTATAATATTAATTAACTAAGTTAT
1 TGTAAGTTATGTA-AATATTAATTAACTAAGTTAT
56269751 GTAATTTATG
Statistics
Matches: 66, Mismatches: 10, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
45 11 0.17
46 1 0.02
47 5 0.08
48 43 0.65
49 5 0.08
50 1 0.02
ACGTcount: A:0.35, C:0.02, G:0.17, T:0.46
Consensus pattern (47 bp):
TGTAAGTTATGTAAATATTAATTAACTAAGTTATAAGTGTTGTAAGT
Found at i:56269779 original size:31 final size:31
Alignment explanation
Indices: 56269708--56269850 Score: 146
Period size: 34 Copynumber: 4.5 Consensus size: 31
56269698 GTTATAAGTT
* *
56269708 ATGTAAG-T-TGTAAGTTATGTATAATATTA
1 ATGTAAGTTATGTAATTTATGTATCATATTA
* *
56269737 ATTAACTAAGTTATGTAATTTATGTATCACATTA
1 A-T--GTAAGTTATGTAATTTATGTATCATATTA
** *
56269771 ATGTAAGTTATGTAACATATGTATAATATTA
1 ATGTAAGTTATGTAATTTATGTATCATATTA
*
56269802 ATTAACTAAGTTATGTAATTTATGTATCATATTA
1 A-T--GTAAGTTATGTAATTTATGTATCATATTA
56269836 ATGTAAGTTATGTAA
1 ATGTAAGTTATGTAA
56269851 CTTACGCATC
Statistics
Matches: 92, Mismatches: 14, Indels: 14
0.77 0.12 0.12
Matches are distributed among these distances:
29 1 0.01
30 1 0.01
31 37 0.40
32 5 0.05
33 3 0.03
34 45 0.49
ACGTcount: A:0.39, C:0.04, G:0.13, T:0.44
Consensus pattern (31 bp):
ATGTAAGTTATGTAATTTATGTATCATATTA
Found at i:56269792 original size:65 final size:65
Alignment explanation
Indices: 56269723--56269851 Score: 249
Period size: 65 Copynumber: 2.0 Consensus size: 65
56269713 AGTTGTAAGT
56269723 TATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATCACATTAATGTAAGTTATGTAACA
1 TATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATCACATTAATGTAAGTTATGTAACA
*
56269788 TATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATCATATTAATGTAAGTTATGTAAC
1 TATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATCACATTAATGTAAGTTATGTAAC
56269852 TTACGCATCG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44
Consensus pattern (65 bp):
TATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATCACATTAATGTAAGTTATGTAACA
Found at i:56274742 original size:41 final size:41
Alignment explanation
Indices: 56274710--56274928 Score: 289
Period size: 41 Copynumber: 5.3 Consensus size: 41
56274700 GCTCAGTTAG
* * * * *
56274710 AAACGCCGTTAAAGATCCGAGCATTGGCGGCGC-TTGTATAA
1 AAACGCCGCTAAAGACCCGAGCATTAGCGGCGCATAG-AAAA
*
56274751 AAACGCCGCTAAAGACCCCAAGCATTAGCGGCGCATAGAAAA
1 AAACGCCGCTAAAGA-CCCGAGCATTAGCGGCGCATAGAAAA
56274793 AAACGCCGCTAAAGACCCGAGCATTAGCGGCGCATAGAAAA
1 AAACGCCGCTAAAGACCCGAGCATTAGCGGCGCATAGAAAA
* * * *
56274834 AAATGCCGCTAAATATCCGAGCATTAGCGGCGCATAGACAA
1 AAACGCCGCTAAAGACCCGAGCATTAGCGGCGCATAGAAAA
* * *
56274875 AAACGCCGC-AAAGACTCGAGCATTAGCGGCGCTTAGACAA
1 AAACGCCGCTAAAGACCCGAGCATTAGCGGCGCATAGAAAA
56274915 AAACGCCGCTAAAG
1 AAACGCCGCTAAAG
56274929 GTTTAAAAAA
Statistics
Matches: 159, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
40 36 0.23
41 88 0.55
42 33 0.21
43 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.24, T:0.14
Consensus pattern (41 bp):
AAACGCCGCTAAAGACCCGAGCATTAGCGGCGCATAGAAAA
Found at i:56274806 original size:83 final size:80
Alignment explanation
Indices: 56274710--56274928 Score: 278
Period size: 83 Copynumber: 2.7 Consensus size: 80
56274700 GCTCAGTTAG
* * *
56274710 AAACGCCGTTAAAGATCCGAGCATTGGCGGCGCTTGTATAAAAACGCCGCTAAAGACCCCAAGCA
1 AAACGCCGCTAAAGA-CCGAGCATTAGCGGCGCTTG-AAAAAAACGCCGCTAAAGA-CCCAAGCA
56274775 TTAGCGGCGCATAGAAAA
63 TTAGCGGCGCATAGAAAA
* * * * *
56274793 AAACGCCGCTAAAGACCCGAGCATTAGCGGCGCATAGAAAAAAATGCCGCTAAATATCCGAGCAT
1 AAACGCCGCTAAAGA-CCGAGCATTAGCGGCGC-TTGAAAAAAACGCCGCTAAAGACCCAAGCAT
*
56274858 TAGCGGCGCATAGACAA
64 TAGCGGCGCATAGAAAA
*
56274875 AAACGCCGC-AAAGACTCGAGCATTAGCGGCGCTTAGACAAAAACGCCGCTAAAG
1 AAACGCCGCTAAAGAC-CGAGCATTAGCGGCGCTT-GAAAAAAACGCCGCTAAAG
56274929 GTTTAAAAAA
Statistics
Matches: 119, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
80 2 0.02
81 37 0.31
82 32 0.27
83 46 0.39
84 2 0.02
ACGTcount: A:0.37, C:0.26, G:0.24, T:0.14
Consensus pattern (80 bp):
AAACGCCGCTAAAGACCGAGCATTAGCGGCGCTTGAAAAAAACGCCGCTAAAGACCCAAGCATTA
GCGGCGCATAGAAAA
Found at i:56275072 original size:40 final size:40
Alignment explanation
Indices: 56274992--56275084 Score: 100
Period size: 40 Copynumber: 2.4 Consensus size: 40
56274982 TTATATAAAA
* **
56274992 CGCCGCTAATTC-CTATTTTTAGCGGCGCTTCGGGATAAT
1 CGCCGCTAATGCTCTACCTTTAGCGGCGCTTCGGGATAAT
* * *
56275031 CGCCGCTGATGCTCTACCTTTAGCGGCGCTT-TGGCTAAAT
1 CGCCGCTAATGCTCTACCTTTAGCGGCGCTTCGGGAT-AAT
*
56275071 CGTCGCTAATGCTC
1 CGCCGCTAATGCTC
56275085 GATTTGTTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
39 13 0.30
40 31 0.70
ACGTcount: A:0.16, C:0.29, G:0.24, T:0.31
Consensus pattern (40 bp):
CGCCGCTAATGCTCTACCTTTAGCGGCGCTTCGGGATAAT
Found at i:56276902 original size:68 final size:66
Alignment explanation
Indices: 56276830--56276981 Score: 144
Period size: 67 Copynumber: 2.2 Consensus size: 66
56276820 TGCTGAACAA
* * * *
56276830 TTCATAGAGGGTCCCAACTATCAATTTTTTGGAGATATGTCTCA-CATCTGTGGAGAGCCATTAA
1 TTCATAGAGGG-CCCAACTATCAA-TTTTTGGACATATGTCTCATC-TCCGTGAAGAGCCACTAA
56276894 ATGG
63 ATGG
* *** * * *
56276898 TTCATGGAAGGGCTTGAGTATCAATTTTTGGACATATGTCTCATCTCCGTGAATAGCCACTGAAT
1 TTCATAG-AGGGCCCAACTATCAATTTTTGGACATATGTCTCATCTCCGTGAAGAGCCACTAAAT
56276963 GG
65 GG
*
56276965 TTCATAGAATGGCCCAA
1 TTCATAG-AGGGCCCAA
56276982 AGGTGACACC
Statistics
Matches: 66, Mismatches: 16, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
67 47 0.71
68 15 0.23
69 4 0.06
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (66 bp):
TTCATAGAGGGCCCAACTATCAATTTTTGGACATATGTCTCATCTCCGTGAAGAGCCACTAAATG
G
Found at i:56277691 original size:92 final size:91
Alignment explanation
Indices: 56277586--56277782 Score: 204
Period size: 90 Copynumber: 2.2 Consensus size: 91
56277576 CTCAAACTTA
** * * * *
56277586 AAAAAAAACAATTAAACCCT-TGCTTTTATTTTGCATTCACTTGGATATA-TAAAAACTTTTAAA
1 AAAAAAAGTAATTAAACCCTCTGCTTTTATTTTGCACTCAATT--AAATACT-AAAACTTTCAAA
*
56277649 ATGCATCAAAAAGGCCCTC-AAATATTTTC
63 ATACATCAAAAAGGCCCTCAAAAT-TTTTC
* * * **
56277678 AAAAAAAGTAATT-AAGCCTCTGGTTTTATTTTTCACTCAATTAAATACTTGAACTTTCAAAATA
1 AAAAAAAGTAATTAAACCCTCTGCTTTTATTTTGCACTCAATTAAATACTAAAACTTTCAAAATA
* *
56277742 CATCGAAAAGGCCCTCAAAATTTTTT
66 CATCAAAAAGGCCCTCAAAATTTTTC
56277768 AAAAAAAGTAATTAA
1 AAAAAAAGTAATTAA
56277783 GCCCCTGATT
Statistics
Matches: 87, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
90 47 0.54
91 11 0.13
92 29 0.33
ACGTcount: A:0.43, C:0.16, G:0.08, T:0.34
Consensus pattern (91 bp):
AAAAAAAGTAATTAAACCCTCTGCTTTTATTTTGCACTCAATTAAATACTAAAACTTTCAAAATA
CATCAAAAAGGCCCTCAAAATTTTTC
Found at i:56277880 original size:20 final size:21
Alignment explanation
Indices: 56277851--56277897 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
56277841 AAAAGACCAT
56277851 TTGACCGTT-AACTTTAACAG
1 TTGACCGTTAAACTTTAACAG
*
56277871 TTGACTGTTAAACTTTAACAG
1 TTGACCGTTAAACTTTAACAG
56277892 TTGACC
1 TTGACC
56277898 ATTCAAATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (21 bp):
TTGACCGTTAAACTTTAACAG
Found at i:56278066 original size:89 final size:89
Alignment explanation
Indices: 56277899--56278142 Score: 280
Period size: 89 Copynumber: 2.7 Consensus size: 89
56277889 CAGTTGACCA
* * *
56277899 TTCAAATACCCAATTGAGTGCAAAAA-AAAATTCGGGGGCTTAATT--TTTTTTAAAAAAGTTTG
1 TTCAAGTACCCAATTGAGTG-AAAAATAAAA-TCAGGGGCTTAATTGCTTTTTTGAAAAAGTTTG
*
56277961 AAGGCCTTTTTTATACAATTTGAAAG
64 AAGGCCTTTTTGATACAATTTGAAAG
* * * **
56277987 TTCAAGTACCCAATTGAGTGAAAAATAAAAGCTGGGGCTTAATTGCATTTTTGAAAAAGTTTGGG
1 TTCAAGTACCCAATTGAGTGAAAAATAAAATCAGGGGCTTAATTGCTTTTTTGAAAAAGTTTGAA
*
56278052 GGTCC-TTTTGATACATTTTGAAAG
66 GG-CCTTTTTGATACAATTTGAAAG
* * * * * *
56278076 TTCAAGTACCAAAGTGAGTGCAAAATAAAATCAAGGGCTTAATGGCTTTTTTTGAAAAATTTTGA
1 TTCAAGTACCCAATTGAGTGAAAAATAAAATCAGGGGCTTAATTGC-TTTTTTGAAAAAGTTTGA
56278141 AG
65 AG
56278143 ACTTTTTACA
Statistics
Matches: 131, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
87 17 0.13
88 23 0.18
89 73 0.56
90 18 0.14
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (89 bp):
TTCAAGTACCCAATTGAGTGAAAAATAAAATCAGGGGCTTAATTGCTTTTTTGAAAAAGTTTGAA
GGCCTTTTTGATACAATTTGAAAG
Found at i:56279637 original size:33 final size:33
Alignment explanation
Indices: 56279595--56279659 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
56279585 GAAAATAATA
56279595 AAATTTTAAAAAATATATTTT-TTAATTAAATTT
1 AAATTTT-AAAAATATATTTTATTAATTAAATTT
* *
56279628 AAATTTTAAAAATATCTTTTATTATTTAAATT
1 AAATTTTAAAAATATATTTTATTAATTAAATT
56279660 GAATTCAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (33 bp):
AAATTTTAAAAATATATTTTATTAATTAAATTT
Found at i:56282322 original size:26 final size:28
Alignment explanation
Indices: 56282288--56282340 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 28
56282278 AACAATCATT
56282288 GCATAGTCATGAATTAAGC-AATGAAAA
1 GCATAGTCATGAATTAAGCAAATGAAAA
*
56282315 GCAT-GTCATGGATTAAGCAAATGAAA
1 GCATAGTCATGAATTAAGCAAATGAAA
56282341 GAAAATTACC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 13 0.54
27 11 0.46
ACGTcount: A:0.45, C:0.11, G:0.21, T:0.23
Consensus pattern (28 bp):
GCATAGTCATGAATTAAGCAAATGAAAA
Found at i:56284103 original size:13 final size:13
Alignment explanation
Indices: 56284085--56284110 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
56284075 ATATTAATGT
56284085 TTTCAAAATTGTA
1 TTTCAAAATTGTA
56284098 TTTCAAAATTGTA
1 TTTCAAAATTGTA
56284111 ATGAGGGATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (13 bp):
TTTCAAAATTGTA
Found at i:56284293 original size:22 final size:22
Alignment explanation
Indices: 56284266--56284310 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
56284256 ATTTTGATTA
56284266 ATATATGTTTAT-ATTAATATTT
1 ATATATGTTTATAATTAA-ATTT
*
56284288 ATATATTTTTATAATTAAATTT
1 ATATATGTTTATAATTAAATTT
56284310 A
1 A
56284311 ATTTTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
ATATATGTTTATAATTAAATTT
Found at i:56293080 original size:41 final size:40
Alignment explanation
Indices: 56293023--56293340 Score: 234
Period size: 41 Copynumber: 7.8 Consensus size: 40
56293013 ATTTTTAAAC
* *
56293023 CTTTAGCGGCGTTTTTA-CTTTAGCGCCGCTAATTCTCCGAT
1 CTTTAGCGGCGTTTTTATC-TGAGCGCCGCTAATTCT-TGAT
* **
56293064 CTTTAGCGGCGTTTTTATCTGAGCGCCACTAATGT-TCTGGC
1 CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAAT-TCT-TGAT
* * * *
56293105 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGTAT
1 CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATTCTTG-AT
* * * * * *
56293146 CATTAGTGGCGTTATTGTCTGAGCGCCACTAATTCTTTGTT
1 CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATTC-TTGAT
* * *
56293187 CTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGTTCGTG-T
1 CTTTAGCGGCGTTTTTATCTGAGCGCCGCT-AA-TTCTTGAT
* * * * **
56293228 TTTTAGTGGCGTTTTTATCTGAGCGCCACTAATACTCTGGC
1 CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATTCT-TGAT
* * * *
56293269 CTTTAGCGGCGTTTTATATGTAAGCGCCGCTAATGC-T-AC
1 CTTTAGCGGCGTTTT-TATCTGAGCGCCGCTAATTCTTGAT
*
56293308 CTTTAGCGGCGTTTTT-TCCGAAGCGCCGCTAAT
1 CTTTAGCGGCGTTTTTATCTG-AGCGCCGCTAAT
56293341 AGTAACAAAA
Statistics
Matches: 221, Mismatches: 45, Indels: 25
0.76 0.15 0.09
Matches are distributed among these distances:
37 1 0.00
38 13 0.06
39 18 0.08
40 6 0.03
41 156 0.71
42 24 0.11
43 3 0.01
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.37
Consensus pattern (40 bp):
CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATTCTTGAT
Found at i:56293167 original size:82 final size:80
Alignment explanation
Indices: 56293022--56293305 Score: 336
Period size: 82 Copynumber: 3.5 Consensus size: 80
56293012 GATTTTTAAA
* * * *
56293022 CCTTTAGCGGCGTTTTTACTTTAGCGCCGCTAATTCTCCG-ATCTTTAGCGGCGTTTTTATCTGA
1 CCTTTAGCGGCGTTTTTTC-TAAGCGCCGCTAATGCT-CGTATCTTTAGTGGCGTTTTTATCTGA
56293086 GCGCCACTAATGTTCTGG
64 GCGCCACTAAT-TTCTGG
* * *
56293104 CCTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGTATCATTAGTGGCGTTATTGTCTGAG
1 CCTTTAGCGGCGTTTTT-TCTAAGCGCCGCTAATGCTCGTATCTTTAGTGGCGTTTTTATCTGAG
* *
56293169 CGCCACTAATTCTTTGT
65 CGCCACTAATT-TCTGG
* * * * *
56293186 TCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGTTCGTGTTTTTAGTGGCGTTTTTATCTGAG
1 CCTTTAGCGGCG-TTTTTTCTAAGCGCCGCTAATGCTCGTATCTTTAGTGGCGTTTTTATCTGAG
*
56293251 CGCCACTAATACTCTGG
65 CGCCACTAAT-TTCTGG
*
56293268 CCTTTAGCGGCGTTTTATATGTAAGCGCCGCTAATGCT
1 CCTTTAGCGGCGTTTT-T-TCTAAGCGCCGCTAATGCT
56293306 ACCTTTAGCG
Statistics
Matches: 171, Mismatches: 24, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
81 7 0.04
82 142 0.83
83 22 0.13
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (80 bp):
CCTTTAGCGGCGTTTTTTCTAAGCGCCGCTAATGCTCGTATCTTTAGTGGCGTTTTTATCTGAGC
GCCACTAATTTCTGG
Found at i:56293280 original size:123 final size:123
Alignment explanation
Indices: 56293021--56293283 Score: 282
Period size: 123 Copynumber: 2.1 Consensus size: 123
56293011 CGATTTTTAA
* * *
56293021 ACCTTTAGCGGCGTTTTTACTTTAGCGCCGCTAATTCTCCGATCTTTAGCGGCGTTTTTATCTGA
1 ACCTTTAGCGGCGTTTTTACTTGAGCGCCACTAATTCTCCGATCTTTAGCGGCGTTTTTATCTAA
* * * *
56293086 GCGCCACTAATGTTCTGGCCTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGT
66 GCGCCACTAAAGTTCTGGCCTTTAGCGGCGTTTTTATCTAAGCGCCACTAATACTCGT
* * * ** * *
56293144 ATCATTAGTGGCGTTATTGT-C-TGAGCGCCACTAATTCTTTGTTCTTTAGCGGCGTTTTTTTCT
1 ACCTTTAGCGGCGTT-TT-TACTTGAGCGCCACTAATTCTCCGATCTTTAGCGGCGTTTTTATCT
* ** * *
56293207 AAGCGCCGCTAAAGTTC-GTGTTTTTAGTGGCGTTTTTATCTGAGCGCCACTAATACTC-T
64 AAGCGCCACTAAAGTTCTG-GCCTTTAGCGGCGTTTTTATCTAAGCGCCACTAATACTCGT
*
56293266 GGCCTTTAGCGGCGTTTT
1 -ACCTTTAGCGGCGTTTT
56293284 ATATGTAAGC
Statistics
Matches: 113, Mismatches: 23, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
122 4 0.04
123 105 0.93
124 3 0.03
125 1 0.01
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.39
Consensus pattern (123 bp):
ACCTTTAGCGGCGTTTTTACTTGAGCGCCACTAATTCTCCGATCTTTAGCGGCGTTTTTATCTAA
GCGCCACTAAAGTTCTGGCCTTTAGCGGCGTTTTTATCTAAGCGCCACTAATACTCGT
Found at i:56293878 original size:15 final size:15
Alignment explanation
Indices: 56293857--56293894 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
56293847 TTTAAGGTTA
56293857 ATTTAGGGGTTGGAG
1 ATTTAGGGGTTGGAG
* *
56293872 GTTTAGGGGTTTGAG
1 ATTTAGGGGTTGGAG
56293887 ATTTAGGG
1 ATTTAGGG
56293895 TTTCAACGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.18, C:0.00, G:0.45, T:0.37
Consensus pattern (15 bp):
ATTTAGGGGTTGGAG
Found at i:56293897 original size:14 final size:14
Alignment explanation
Indices: 56293830--56293897 Score: 52
Period size: 15 Copynumber: 4.9 Consensus size: 14
56293820 GACTGGGTAT
*
56293830 AGATTTAAGGTTTG
1 AGATTTAGGGTTTG
* *
56293844 GGATTTAAGG-TT-
1 AGATTTAGGGTTTG
*
56293856 A-ATTTAGGGGTTGG
1 AGATTTA-GGGTTTG
*
56293870 AGGTTTAGGGGTTTG
1 AGATTTA-GGGTTTG
56293885 AGATTTAGGGTTT
1 AGATTTAGGGTTT
56293898 CAACGGTCAT
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
11 5 0.12
12 2 0.05
13 3 0.07
14 16 0.37
15 17 0.40
ACGTcount: A:0.22, C:0.00, G:0.37, T:0.41
Consensus pattern (14 bp):
AGATTTAGGGTTTG
Found at i:56295618 original size:8 final size:10
Alignment explanation
Indices: 56295596--56295632 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
56295586 TATTTTTACT
56295596 TATATATGGA
1 TATATATGGA
*
56295606 TATATATGAA
1 TATATATGGA
56295616 TATATATGGA
1 TATATATGGA
56295626 TATATAT
1 TATATAT
56295633 ATAGTTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (10 bp):
TATATATGGA
Found at i:56298282 original size:13 final size:13
Alignment explanation
Indices: 56298264--56298288 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56298254 CAACATAATA
56298264 CATAACTTACATT
1 CATAACTTACATT
56298277 CATAACTTACAT
1 CATAACTTACAT
56298289 AAACTTATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (13 bp):
CATAACTTACATT
Found at i:56298396 original size:34 final size:33
Alignment explanation
Indices: 56298353--56298533 Score: 134
Period size: 34 Copynumber: 5.7 Consensus size: 33
56298343 GGGTGATGTG
56298353 ATATTATACATAAATTACATAACTTAATTAATTA
1 ATATTATACATAAATTACATAA-TTAATTAATTA
*
56298387 ATATTATACATAACTTAC---ATTAA-T-ATT-
1 ATATTATACATAAATTACATAATTAATTAATTA
* * * *
56298414 ATA-CATAAATTACA-T--A-ACTTAATTAATTA
1 ATATTATACA-TAAATTACATAATTAATTAATTA
* * *
56298443 ATATTATACATAACTTACATTAA-TATTATACATAA
1 ATATTATACATAAATTACA-TAATTAAT-TA-ATTA
*
56298478 ATATTATACATAAATTACATAACTTAGTTAATTA
1 ATATTATACATAAATTACATAA-TTAATTAATTA
*
56298512 ATATTATACATAACTTACATAA
1 ATATTATACATAAATTACATAA
56298534 CATTTTAACA
Statistics
Matches: 114, Mismatches: 17, Indels: 32
0.70 0.10 0.20
Matches are distributed among these distances:
26 9 0.08
27 6 0.05
28 6 0.05
29 6 0.05
30 9 0.08
31 1 0.01
32 1 0.01
33 3 0.03
34 47 0.41
35 23 0.20
36 3 0.03
ACGTcount: A:0.49, C:0.10, G:0.01, T:0.40
Consensus pattern (33 bp):
ATATTATACATAAATTACATAATTAATTAATTA
Found at i:56298411 original size:22 final size:22
Alignment explanation
Indices: 56298378--56298428 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
56298368 TACATAACTT
56298378 AATTA-ATTAATATTATACATA
1 AATTACATTAATATTATACATA
*
56298399 ACTTACATTAATATTATACATA
1 AATTACATTAATATTATACATA
56298421 AATTACAT
1 AATTACAT
56298429 AACTTAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 4 0.15
22 23 0.85
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (22 bp):
AATTACATTAATATTATACATA
Found at i:56298480 original size:13 final size:13
Alignment explanation
Indices: 56298458--56298492 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
56298448 ATACATAACT
*
56298458 TACATTAATATTA
1 TACATAAATATTA
56298471 TACATAAATATTA
1 TACATAAATATTA
56298484 TACATAAAT
1 TACATAAAT
56298493 TACATAACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (13 bp):
TACATAAATATTA
Found at i:56298481 original size:69 final size:69
Alignment explanation
Indices: 56298402--56298531 Score: 242
Period size: 69 Copynumber: 1.9 Consensus size: 69
56298392 ATACATAACT
*
56298402 TACATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTACATTAAT
1 TACATAAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTACATTAAT
56298467 ATTA
66 ATTA
*
56298471 TACATAAATATTATACATAAATTACATAACTTAGTTAATTAATATTATACATAACTTACAT
1 TACATAAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTACAT
56298532 AACATTTTAA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 59 1.00
ACGTcount: A:0.48, C:0.11, G:0.01, T:0.41
Consensus pattern (69 bp):
TACATAAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTACATTAAT
ATTA
Found at i:56298494 original size:56 final size:56
Alignment explanation
Indices: 56298353--56298479 Score: 254
Period size: 56 Copynumber: 2.3 Consensus size: 56
56298343 GGGTGATGTG
56298353 ATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTACATTA
1 ATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTACATTA
56298409 ATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTACATTA
1 ATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTACATTA
56298465 ATATTATACATAAAT
1 ATATTATACATAAAT
56298480 ATTATACATA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 71 1.00
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (56 bp):
ATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTACATTA
Found at i:56298534 original size:34 final size:34
Alignment explanation
Indices: 56298405--56298534 Score: 174
Period size: 34 Copynumber: 3.8 Consensus size: 34
56298395 CATAACTTAC
56298405 ATTAATATTATACATAAATTACATAACTTAATTA
1 ATTAATATTATACATAAATTACATAACTTAATTA
* *
56298439 ATTAATATTATACATAACTTACATTAA--TATTATA
1 ATTAATATTATACATAAATTACA-TAACTTAAT-TA
* *
56298473 CATAAATATTATACATAAATTACATAACTTAGTTA
1 -ATTAATATTATACATAAATTACATAACTTAATTA
*
56298508 ATTAATATTATACATAACTTACATAAC
1 ATTAATATTATACATAAATTACATAAC
56298535 ATTTTAACAA
Statistics
Matches: 84, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
33 3 0.04
34 52 0.62
35 26 0.31
36 3 0.04
ACGTcount: A:0.48, C:0.11, G:0.01, T:0.40
Consensus pattern (34 bp):
ATTAATATTATACATAAATTACATAACTTAATTA
Found at i:56298571 original size:9 final size:9
Alignment explanation
Indices: 56298557--56298687 Score: 70
Period size: 9 Copynumber: 15.9 Consensus size: 9
56298547 TGCATAATAA
56298557 ATAACTTAC
1 ATAACTTAC
56298566 ATAACTTAC
1 ATAACTTAC
56298575 ATAA--TAC
1 ATAACTTAC
*
56298582 ATAACTTAT
1 ATAACTTAC
* *
56298591 ATGACTTAT
1 ATAACTTAC
56298600 ATAACTTAC
1 ATAACTTAC
*
56298609 AT-A---GC
1 ATAACTTAC
* *
56298614 ATAATTTTC
1 ATAACTTAC
56298623 ATAA--TAC
1 ATAACTTAC
*
56298630 ACAACTTAC
1 ATAACTTAC
** *
56298639 ATAGTTTTC
1 ATAACTTAC
*
56298648 ATAA--TAA
1 ATAACTTAC
56298655 ATAACTTAC
1 ATAACTTAC
56298664 ATAA--TAC
1 ATAACTTAC
56298671 ATAACTTAC
1 ATAACTTAC
*
56298680 ATAGCTTA
1 ATAACTTA
56298688 ATTATACTTA
Statistics
Matches: 93, Mismatches: 17, Indels: 24
0.69 0.13 0.18
Matches are distributed among these distances:
5 3 0.03
6 1 0.01
7 24 0.26
8 1 0.01
9 64 0.69
ACGTcount: A:0.44, C:0.17, G:0.03, T:0.36
Consensus pattern (9 bp):
ATAACTTAC
Found at i:56298578 original size:25 final size:25
Alignment explanation
Indices: 56298549--56298674 Score: 91
Period size: 25 Copynumber: 5.2 Consensus size: 25
56298539 TAACAATTTG
56298549 CATAATAAATAACTTACATAACTTA
1 CATAATAAATAACTTACATAACTTA
* * *
56298574 CATAATACATAACTTATATGACTT-
1 CATAATAAATAACTTACATAACTTA
* * * * *
56298598 -AT-ATAACTTACATAGCATAATTTT
1 CATAATAAATAACTTA-CATAACTTA
* * ** *
56298622 CATAATACACAACTTACATAGTTTT
1 CATAATAAATAACTTACATAACTTA
56298647 CATAATAAATAACTTACATAA--TA
1 CATAATAAATAACTTACATAACTTA
56298670 CATAA
1 CATAA
56298675 CTTACATAGC
Statistics
Matches: 77, Mismatches: 20, Indels: 10
0.72 0.19 0.09
Matches are distributed among these distances:
22 8 0.10
23 13 0.17
25 49 0.64
26 7 0.09
ACGTcount: A:0.47, C:0.16, G:0.02, T:0.35
Consensus pattern (25 bp):
CATAATAAATAACTTACATAACTTA
Found at i:56298582 original size:16 final size:16
Alignment explanation
Indices: 56298563--56298682 Score: 78
Period size: 16 Copynumber: 7.9 Consensus size: 16
56298553 ATAAATAACT
56298563 TACATAACTTACATAA
1 TACATAACTTACATAA
* *
56298579 TACATAACTTATATGACT
1 TACATAACTTACAT-A-A
*
56298597 TATATAACTTACAT-A
1 TACATAACTTACATAA
* * *
56298612 -GCATAATTTTCATAA
1 TACATAACTTACATAA
* *
56298627 TACACAACTTACATAG
1 TACATAACTTACATAA
56298643 T---T---TT-CATAA
1 TACATAACTTACATAA
*
56298652 TAAATAACTTACATAA
1 TACATAACTTACATAA
56298668 TACATAACTTACATA
1 TACATAACTTACATA
56298683 GCTTAATTAT
Statistics
Matches: 76, Mismatches: 17, Indels: 22
0.66 0.15 0.19
Matches are distributed among these distances:
9 5 0.07
10 2 0.03
12 1 0.01
14 9 0.12
15 3 0.04
16 43 0.57
17 1 0.01
18 12 0.16
ACGTcount: A:0.45, C:0.17, G:0.03, T:0.36
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:56304269 original size:66 final size:66
Alignment explanation
Indices: 56304133--56304277 Score: 177
Period size: 66 Copynumber: 2.2 Consensus size: 66
56304123 GGCAACATCG
* *
56304133 AGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGCTACAACTGAAAGCAGATGTAGTAGC
1 AGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGCTACAACTGAAAGCAGATGCAGCAGC
*
56304198 G
66 A
* * * * *
56304199 AGAGAAGCTGAGGTTCAACGAAAG-TATGAAGAACTCCAGC-AGCAGCTTAAAGTAGATGCGGCA
1 AGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCAGCTA-CAACTGAAAGCAGATGCAGCA
56304262 GCA
64 GCA
*
56304265 AGAGAAGCAGAGG
1 AGAGAAGCTGAGG
56304278 CGGCAGCTAG
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
65 1 0.01
66 63 0.93
67 4 0.06
ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14
Consensus pattern (66 bp):
AGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGCTACAACTGAAAGCAGATGCAGCAGC
A
Found at i:56304321 original size:21 final size:21
Alignment explanation
Indices: 56304260--56304360 Score: 103
Period size: 21 Copynumber: 4.8 Consensus size: 21
56304250 GTAGATGCGG
* **
56304260 CAGCAAGAGAAGCAGAGGCGG
1 CAGCGAGAGAAGCAGAGGCTA
* * *
56304281 CAGCTAGAGAAGTACAGGCTA
1 CAGCGAGAGAAGCAGAGGCTA
56304302 CAGCGAGAGAAGCAGAGGCTA
1 CAGCGAGAGAAGCAGAGGCTA
* * * *
56304323 AAGCGAGGGAAGCAGAGGTTG
1 CAGCGAGAGAAGCAGAGGCTA
*
56304344 CAGCGAGGGAAGCAGAG
1 CAGCGAGAGAAGCAGAG
56304361 CAGCGTCAAA
Statistics
Matches: 67, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 67 1.00
ACGTcount: A:0.37, C:0.17, G:0.41, T:0.06
Consensus pattern (21 bp):
CAGCGAGAGAAGCAGAGGCTA
Found at i:56304751 original size:43 final size:43
Alignment explanation
Indices: 56304704--56305059 Score: 304
Period size: 43 Copynumber: 8.3 Consensus size: 43
56304694 AGGTGTTGGC
* *
56304704 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGT
1 CTTTAGCGGCGTTTTTGGTCAAAGCGCCGCTAAAGATCAGGGT
* ** * *
56304747 CTTTAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGATCATGGT
1 CTTTAGCGGCGTTTTTGGTCAAAGCGCCGCTAAAGATCAGGGT
** * *
56304790 CTTTAGCGGCGTTTTTGGGGAAAGCGCCGCTAAAGATTAGGTT
1 CTTTAGCGGCGTTTTTGGTCAAAGCGCCGCTAAAGATCAGGGT
** * *
56304833 CTTTAGTAGCGTTTTGTGGTCGAAGCGCCGCTATAGATCAGGGT
1 CTTTAGCGGCGTTTT-TGGTCAAAGCGCCGCTAAAGATCAGGGT
* ** * *
56304877 CTATT-GCGGCGTTTTAGGGGAAAGCGCCGCTAAAGATTAGGTT
1 CT-TTAGCGGCGTTTTTGGTCAAAGCGCCGCTAAAGATCAGGGT
* * * *
56304920 CTTTCGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGGT
1 CTTTAGCGGCGTTTTTGGTCAAAGCGCCGCTAAAGATCAGGGT
** *** * * * ** *
56304963 CTATT-GCGGCGTTTGAGAAAAAAACGCCGCTAAATACCCTGAT
1 CT-TTAGCGGCGTTTTTGGTCAAAGCGCCGCTAAAGATCAGGGT
* * * *
56305006 CTTTAGCGGCGCTTCTAG-CACAAACGCCGCTAAAGATCAGGGT
1 CTTTAGCGGCGTTTTTGGTCA-AAGCGCCGCTAAAGATCAGGGT
56305049 CTTTAGCGGCG
1 CTTTAGCGGCG
56305060 CTTCCACTAA
Statistics
Matches: 245, Mismatches: 62, Indels: 12
0.77 0.19 0.04
Matches are distributed among these distances:
42 5 0.02
43 204 0.83
44 34 0.14
45 2 0.01
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (43 bp):
CTTTAGCGGCGTTTTTGGTCAAAGCGCCGCTAAAGATCAGGGT
Found at i:56304876 original size:130 final size:129
Alignment explanation
Indices: 56304704--56304956 Score: 323
Period size: 130 Copynumber: 2.0 Consensus size: 129
56304694 AGGTGTTGGC
*
56304704 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGTCT-TTAGCGGCGTTTGT-GGAA
1 CTTTAGTAGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGTCTATT-GCGGCGTTT-TAGGAA
* *
56304767 AAAGCGCCACTAAAGATCATGG-TCTTTAGCGGCGTTTTTGGGGAAAGCGCCGCTAAAGATTAGG
64 AAAGCGCCACTAAAGATCA-GGTTCTTTAGCGGCGTTTGTGGGCAAAGCGCCGCTAAAGATTAGG
56304831 TT
128 TT
* * * **
56304833 CTTTAGTAGCGTTTTGTGGTCGAAGCGCCGCTATAGATCAGGGTCTATTGCGGCGTTTTAGGGGA
1 CTTTAGTAGCGTTTT-TGGTCAAAGCGCCGCTAAAGATAAGGGTCTATTGCGGCGTTTTAGGAAA
* * * * * *
56304898 AAGCGCCGCTAAAGATTAGGTTCTTTCGTGGCGTTTGTGGTCAAAGCGCCGCTATAGAT
65 AAGCGCCACTAAAGATCAGGTTCTTTAGCGGCGTTTGTGGGCAAAGCGCCGCTAAAGAT
56304957 CAGGGTCTAT
Statistics
Matches: 106, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
129 17 0.16
130 87 0.82
131 2 0.02
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.30
Consensus pattern (129 bp):
CTTTAGTAGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGTCTATTGCGGCGTTTTAGGAAAA
AGCGCCACTAAAGATCAGGTTCTTTAGCGGCGTTTGTGGGCAAAGCGCCGCTAAAGATTAGGTT
Found at i:56304996 original size:86 final size:86
Alignment explanation
Indices: 56304724--56304976 Score: 373
Period size: 86 Copynumber: 2.9 Consensus size: 86
56304714 GTTTTTGGTC
* * * ** * * *
56304724 AAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGATCATGG
1 AAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGG
*
56304789 TCT-TTAGCGGCGTTTTTGGGG
66 TCTATT-GCGGCGTTTTAGGGG
* *
56304810 AAAGCGCCGCTAAAGATTAGGTTCTTTAGTAGCGTTTTGTGGTCGAAGCGCCGCTATAGATCAGG
1 AAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCG-TTTGTGGTCAAAGCGCCGCTATAGATCAGG
56304875 GTCTATTGCGGCGTTTTAGGGG
65 GTCTATTGCGGCGTTTTAGGGG
*
56304897 AAAGCGCCGCTAAAGATTAGGTTCTTTCGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGG
1 AAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGG
56304962 TCTATTGCGGCGTTT
66 TCTATTGCGGCGTTT
56304977 GAGAAAAAAA
Statistics
Matches: 151, Mismatches: 14, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
86 75 0.50
87 74 0.49
88 2 0.01
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.28
Consensus pattern (86 bp):
AAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGG
TCTATTGCGGCGTTTTAGGGG
Found at i:56306755 original size:33 final size:32
Alignment explanation
Indices: 56306712--56306823 Score: 145
Period size: 27 Copynumber: 3.8 Consensus size: 32
56306702 ATTTAATGCC
56306712 TTACTGGTGTGTTTGGGAGGATTATGATATAT
1 TTACTGGTGTGTTTGGGAGGATTATGATATAT
56306744 TATACTGGTGTGTTTGGGAGGA-TAT-AT-TAT
1 T-TACTGGTGTGTTTGGGAGGATTATGATATAT
56306774 TT--TGGTGTGTTTGGGAGGATTATGATATA-
1 TTACTGGTGTGTTTGGGAGGATTATGATATAT
56306803 -T--TGGTGTGTTT-GGAGGATTAT
1 TTACTGGTGTGTTTGGGAGGATTAT
56306824 ATTATTCTAG
Statistics
Matches: 76, Mismatches: 0, Indels: 13
0.85 0.00 0.15
Matches are distributed among these distances:
27 27 0.36
28 14 0.18
29 3 0.04
30 6 0.08
31 2 0.03
32 4 0.05
33 20 0.26
ACGTcount: A:0.21, C:0.02, G:0.33, T:0.45
Consensus pattern (32 bp):
TTACTGGTGTGTTTGGGAGGATTATGATATAT
Found at i:56307146 original size:21 final size:21
Alignment explanation
Indices: 56307120--56307160 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
56307110 GAAAATTCGT
*
56307120 ATAAGAATGAAA-AATTTGAAC
1 ATAAG-ATGAAATAATATGAAC
56307141 ATAAGATGAAATAATATGAA
1 ATAAGATGAAATAATATGAA
56307161 AAGTATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.59, C:0.02, G:0.15, T:0.24
Consensus pattern (21 bp):
ATAAGATGAAATAATATGAAC
Found at i:56312203 original size:28 final size:28
Alignment explanation
Indices: 56312144--56312208 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
56312134 AATCTTTTCC
* *
56312144 TTTACATTTGAACTAAAGCAATTTTTAAT
1 TTTA-ATTTCAACTAAAACAATTTTTAAT
*
56312173 TTTTATTTCAACTAAAACAATTTTTAAT
1 TTTAATTTCAACTAAAACAATTTTTAAT
56312201 TTTAATTT
1 TTTAATTT
56312209 TTAATAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 29 0.91
29 3 0.09
ACGTcount: A:0.37, C:0.09, G:0.03, T:0.51
Consensus pattern (28 bp):
TTTAATTTCAACTAAAACAATTTTTAAT
Found at i:56314436 original size:30 final size:32
Alignment explanation
Indices: 56314376--56314438 Score: 85
Period size: 30 Copynumber: 2.0 Consensus size: 32
56314366 AAAACCAATT
*
56314376 AAATCTCCATCTAACATATCCATAAGAAAAAA
1 AAATCTCCATCTAACATATCCATAACAAAAAA
* *
56314408 AAATCTCCATCT-A-ATATCTATACCAAAAAA
1 AAATCTCCATCTAACATATCCATAACAAAAAA
56314438 A
1 A
56314439 TATAAAATAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 15 0.54
31 1 0.04
32 12 0.43
ACGTcount: A:0.52, C:0.22, G:0.02, T:0.24
Consensus pattern (32 bp):
AAATCTCCATCTAACATATCCATAACAAAAAA
Found at i:56317318 original size:21 final size:22
Alignment explanation
Indices: 56317292--56317338 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
56317282 CTCTGCTCAA
*
56317292 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
56317313 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
56317335 ACTC
1 ACTC
56317339 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:56324072 original size:8 final size:8
Alignment explanation
Indices: 56324037--56324083 Score: 58
Period size: 8 Copynumber: 5.6 Consensus size: 8
56324027 GGTATGTTCA
56324037 TTTCTTCT
1 TTTCTTCT
56324045 TCTTCTTCT
1 T-TTCTTCT
*
56324054 TTTCTCCCT
1 TTTCT-TCT
*
56324063 TTTTTTCT
1 TTTCTTCT
56324071 TTTCTTCT
1 TTTCTTCT
56324079 TTTCT
1 TTTCT
56324084 GCTGCCTTGC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
8 19 0.58
9 14 0.42
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (8 bp):
TTTCTTCT
Found at i:56325825 original size:3 final size:3
Alignment explanation
Indices: 56325817--56325845 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
56325807 ACCCATGCAA
56325817 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
56325846 AGATATAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:56325880 original size:6 final size:6
Alignment explanation
Indices: 56325871--56325988 Score: 119
Period size: 6 Copynumber: 19.7 Consensus size: 6
56325861 TGAAAATTTT
* * * * * * * *
56325871 AGATAC AGATGC AGTTAT AGATAT AAATAC ATATAC ATATAC ATATAC
1 AGATAC AGATAC AGATAC AGATAC AGATAC AGATAC AGATAC AGATAC
* * *
56325919 AGATAC AGATAC AGATAC AGGTAC AGATAC AGATGC AAATAC AGATAC
1 AGATAC AGATAC AGATAC AGATAC AGATAC AGATAC AGATAC AGATAC
* *
56325967 AGATAC AGATAT AGATAT AGAT
1 AGATAC AGATAC AGATAC AGAT
56325989 GTAGATATAG
Statistics
Matches: 96, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 96 1.00
ACGTcount: A:0.48, C:0.13, G:0.15, T:0.24
Consensus pattern (6 bp):
AGATAC
Found at i:56325993 original size:6 final size:6
Alignment explanation
Indices: 56325886--56326000 Score: 54
Period size: 6 Copynumber: 19.2 Consensus size: 6
56325876 CAGATGCAGT
* * * * *
56325886 TATAGA TATA-A -ATACA TATACA TATACA TATACAGA TACAGA TACAGA
1 TATAGA TATAGA TATAGA TATAGA TATAGA TAT--AGA TATAGA TATAGA
* * * * ** * * * *
56325934 TACAGG TACAGA TACAGA TGCAAA TACAGA TACAGA TACAGA TATAGA
1 TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA
*
56325982 TATAGA TGTAGA TATAGA T
1 TATAGA TATAGA TATAGA T
56326001 CCTACCATCA
Statistics
Matches: 94, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
4 3 0.03
5 2 0.02
6 85 0.90
8 4 0.04
ACGTcount: A:0.49, C:0.11, G:0.15, T:0.25
Consensus pattern (6 bp):
TATAGA
Found at i:56329802 original size:43 final size:44
Alignment explanation
Indices: 56329736--56329852 Score: 150
Period size: 44 Copynumber: 2.7 Consensus size: 44
56329726 AGCTGATACA
* * *
56329736 ATGCCAACGTCCCAGATGTGGTCTTACATGT-AATTACATATCG
1 ATGCCAACGTCCCAGATGTGGTCTTACACGTAAATCACAAATCG
56329779 ATGCC-ACTGTCCCAGATAG-GGTCTTACACGTAAATCACAAATCG
1 ATGCCAAC-GTCCCAGAT-GTGGTCTTACACGTAAATCACAAATCG
* *
56329823 ATGCGAACGTCCCAGACGTGGTCTTACACG
1 ATGCCAACGTCCCAGATGTGGTCTTACACG
56329853 ATAACACACA
Statistics
Matches: 64, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
42 2 0.03
43 26 0.41
44 34 0.53
45 2 0.03
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (44 bp):
ATGCCAACGTCCCAGATGTGGTCTTACACGTAAATCACAAATCG
Found at i:56330784 original size:15 final size:14
Alignment explanation
Indices: 56330747--56330790 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
56330737 TTTTATTATA
56330747 ATAACTTTATAATAT
1 ATAACTTTATAAT-T
*
56330762 ATAA-TTTATTATT
1 ATAACTTTATAATT
56330775 ATAACCTTTATAATT
1 ATAA-CTTTATAATT
56330790 A
1 A
56330791 ATATAAAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 5 0.20
14 7 0.28
15 13 0.52
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (14 bp):
ATAACTTTATAATT
Found at i:56332991 original size:13 final size:13
Alignment explanation
Indices: 56332973--56333011 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 13
56332963 AATTTTTATT
*
56332973 TATTTATAAAATA
1 TATTTATAAAAAA
56332986 TATTTATAAAAAAA
1 TATTTAT-AAAAAA
56333000 TATTT-TAAAAAA
1 TATTTATAAAAAA
56333012 ATCAAATGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 6 0.25
13 8 0.33
14 10 0.42
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TATTTATAAAAAA
Found at i:56333002 original size:14 final size:14
Alignment explanation
Indices: 56332973--56333013 Score: 59
Period size: 13 Copynumber: 3.1 Consensus size: 14
56332963 AATTTTTATT
*
56332973 TATTTAT-AAAATA
1 TATTTATAAAAAAA
56332986 TATTTATAAAAAAA
1 TATTTATAAAAAAA
56333000 TATTT-TAAAAAAA
1 TATTTATAAAAAAA
56333013 T
1 T
56333014 CAAATGTGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 16 0.62
14 10 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TATTTATAAAAAAA
Found at i:56333803 original size:20 final size:20
Alignment explanation
Indices: 56333778--56333820 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
56333768 CGAAAAATGA
56333778 TTTCTGGAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
56333798 TTTCTGGAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
56333818 TTT
1 TTT
56333821 TTGGTGTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.28, C:0.09, G:0.14, T:0.49
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:56335192 original size:32 final size:32
Alignment explanation
Indices: 56335143--56335235 Score: 150
Period size: 32 Copynumber: 2.9 Consensus size: 32
56335133 TGTCAATCAT
56335143 TTCAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATCCAACAAGCTTAAAACATAATAAA
* *
56335175 TTCAATATCGAATAAGCTTAAAACATAATAAA
1 TTCAATATCCAACAAGCTTAAAACATAATAAA
* *
56335207 TTCAACATCTAACAAGCTTAAAACATAAT
1 TTCAATATCCAACAAGCTTAAAACATAAT
56335236 CAATATCTAA
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 56 1.00
ACGTcount: A:0.52, C:0.17, G:0.04, T:0.27
Consensus pattern (32 bp):
TTCAATATCCAACAAGCTTAAAACATAATAAA
Found at i:56335254 original size:16 final size:16
Alignment explanation
Indices: 56335235--56335291 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
56335225 TAAAACATAA
56335235 TCAATATCTAACAAAT
1 TCAATATCTAACAAAT
* * *
56335251 TCAAGA-CATAATAATT
1 TCAATATC-TAACAAAT
*
56335267 TCAAAATCTAACAAATT
1 TCAATATCTAACAAA-T
56335284 TCAATATC
1 TCAATATC
56335292 ATTATCCAAC
Statistics
Matches: 31, Mismatches: 7, Indels: 5
0.72 0.16 0.12
Matches are distributed among these distances:
15 1 0.03
16 21 0.68
17 9 0.29
ACGTcount: A:0.49, C:0.18, G:0.02, T:0.32
Consensus pattern (16 bp):
TCAATATCTAACAAAT
Found at i:56341245 original size:22 final size:21
Alignment explanation
Indices: 56341217--56341274 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
56341207 ACTTACCAAG
*
56341217 CAAGTCTCAAGACATCATGAC
1 CAAGTCTCAAGACATAATGAC
56341238 TCAAGTCTTC-AGACATAATGAC
1 -CAAGTC-TCAAGACATAATGAC
56341260 CTAAGTCTCAAGACA
1 C-AAGTCTCAAGACA
56341275 ACAAAATATT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 3 0.09
22 27 0.84
23 2 0.06
ACGTcount: A:0.38, C:0.26, G:0.14, T:0.22
Consensus pattern (21 bp):
CAAGTCTCAAGACATAATGAC
Found at i:56345286 original size:11 final size:11
Alignment explanation
Indices: 56345270--56345294 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
56345260 TTAAGTATGT
56345270 ATGTACGGTTC
1 ATGTACGGTTC
56345281 ATGTACGGTTC
1 ATGTACGGTTC
56345292 ATG
1 ATG
56345295 GGTGAAGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.16, G:0.28, T:0.36
Consensus pattern (11 bp):
ATGTACGGTTC
Found at i:56350954 original size:16 final size:16
Alignment explanation
Indices: 56350933--56350966 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
56350923 AAAAAATCCA
56350933 CTTCCACTTTTTTCAG
1 CTTCCACTTTTTTCAG
56350949 CTTCCACTTTTTTCAG
1 CTTCCACTTTTTTCAG
56350965 CT
1 CT
56350967 ACTTGTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.12, C:0.32, G:0.06, T:0.50
Consensus pattern (16 bp):
CTTCCACTTTTTTCAG
Found at i:56357346 original size:20 final size:21
Alignment explanation
Indices: 56357308--56357346 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
56357298 AATATTTTTA
* *
56357308 AAAACAATTATAATTAGATGG
1 AAAACAATTAAAATCAGATGG
56357329 AAAA-AATTAAAATCAGAT
1 AAAACAATTAAAATCAGAT
56357347 AAAATAAACG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.59, C:0.05, G:0.10, T:0.26
Consensus pattern (21 bp):
AAAACAATTAAAATCAGATGG
Found at i:56357490 original size:22 final size:22
Alignment explanation
Indices: 56357459--56357501 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
56357449 GAAGTTGATG
* *
56357459 TTTATTAAAATTTAATATATAT
1 TTTATAAAAATTTAAAATATAT
56357481 TTTATAAAAATTTAAAATATA
1 TTTATAAAAATTTAAAATATA
56357502 AATAAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTATAAAAATTTAAAATATAT
Found at i:56369647 original size:21 final size:21
Alignment explanation
Indices: 56369617--56369658 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
56369607 GCATGCCCAT
56369617 ATTATTTTATAT-TTTTTAAA
1 ATTATTTTATATATTTTTAAA
56369637 ATTATATTTATATGATTTTTAA
1 ATTAT-TTTATAT-ATTTTTAA
56369659 TTTAATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.26
21 7 0.37
23 7 0.37
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (21 bp):
ATTATTTTATATATTTTTAAA
Found at i:56369679 original size:23 final size:22
Alignment explanation
Indices: 56369619--56369685 Score: 57
Period size: 23 Copynumber: 3.0 Consensus size: 22
56369609 ATGCCCATAT
* *
56369619 TATTTTATATTTTTTAAAATTA
1 TATTTAATATTTTTTAAATTTA
56369641 TATTT-ATATGATTTTT-AATTTAA
1 TATTTAATAT--TTTTTAAATTT-A
*
56369664 TATTTAATAATTTTTTGAATTT
1 TATTTAAT-ATTTTTTAAATTT
56369686 TTAAAATTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
21 4 0.11
22 9 0.24
23 16 0.42
24 7 0.18
25 2 0.05
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (22 bp):
TATTTAATATTTTTTAAATTTA
Found at i:56372339 original size:9 final size:9
Alignment explanation
Indices: 56372316--56372347 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
56372306 AGAATAGTAT
56372316 TAATAATGA
1 TAATAATGA
56372325 -AA-AATGA
1 TAATAATGA
56372332 TAATAATGA
1 TAATAATGA
56372341 TAATAAT
1 TAATAAT
56372348 AATGAAGGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
7 5 0.24
8 4 0.19
9 12 0.57
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.31
Consensus pattern (9 bp):
TAATAATGA
Found at i:56373714 original size:17 final size:17
Alignment explanation
Indices: 56373694--56373726 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
56373684 TATTTGGACT
*
56373694 TTTTATTTATTTTTTGG
1 TTTTATTTATTATTTGG
56373711 TTTTATTTATTATTTG
1 TTTTATTTATTATTTG
56373727 TATTTGGTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.09, T:0.76
Consensus pattern (17 bp):
TTTTATTTATTATTTGG
Found at i:56374800 original size:20 final size:20
Alignment explanation
Indices: 56374750--56374800 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
56374740 TAAATAAATT
*
56374750 TATAATTTATAATTTATAAC
1 TATAATTTTTAATTTATAAC
* * * *
56374770 TAAAATATTTAATTTTTTAC
1 TATAATTTTTAATTTATAAC
56374790 TATAATTTTTA
1 TATAATTTTTA
56374801 TTCTTAATTA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (20 bp):
TATAATTTTTAATTTATAAC
Found at i:56375225 original size:16 final size:16
Alignment explanation
Indices: 56375204--56375256 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 16
56375194 AAAATATACA
56375204 AAAAATAATTAATTAC
1 AAAAATAATTAATTAC
*
56375220 AAAAATAA-T-A-T-G
1 AAAAATAATTAATTAC
56375232 AAAAATAAATTAATTAC
1 AAAAAT-AATTAATTAC
*
56375249 AACAATAA
1 AAAAATAA
56375257 ACATTTGCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 10
0.69 0.07 0.24
Matches are distributed among these distances:
12 6 0.21
13 3 0.10
14 2 0.07
15 2 0.07
16 11 0.38
17 5 0.17
ACGTcount: A:0.66, C:0.06, G:0.02, T:0.26
Consensus pattern (16 bp):
AAAAATAATTAATTAC
Found at i:56375365 original size:24 final size:24
Alignment explanation
Indices: 56375338--56375385 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
56375328 AATATTCAAA
56375338 GACTTGATATATAAATTTTTCATT
1 GACTTGATATATAAATTTTTCATT
*
56375362 GACTTGATATGTAAATTTTTCATT
1 GACTTGATATATAAATTTTTCATT
56375386 TTGATTAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.50
Consensus pattern (24 bp):
GACTTGATATATAAATTTTTCATT
Found at i:56380272 original size:26 final size:28
Alignment explanation
Indices: 56380237--56380289 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 28
56380227 GGTAATTTTC
56380237 TTTCATTTGCTTAATCCATGAC-ATGCT
1 TTTCATTTGCTTAATCCATGACTATGCT
*
56380264 TTTCA-TTGCTTAATTCATGACTATGC
1 TTTCATTTGCTTAATCCATGACTATGC
56380290 AATGATTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 15 0.62
27 9 0.38
ACGTcount: A:0.23, C:0.21, G:0.11, T:0.45
Consensus pattern (28 bp):
TTTCATTTGCTTAATCCATGACTATGCT
Found at i:56382533 original size:14 final size:14
Alignment explanation
Indices: 56382514--56382542 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
56382504 CCGTCCCGAG
56382514 TATGTCTGTAAGCA
1 TATGTCTGTAAGCA
56382528 TATGTCTGTAAGCA
1 TATGTCTGTAAGCA
56382542 T
1 T
56382543 GTTTGTAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.38
Consensus pattern (14 bp):
TATGTCTGTAAGCA
Found at i:56384776 original size:10 final size:10
Alignment explanation
Indices: 56384761--56384788 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
56384751 TCTTTGGCTC
56384761 ATATATAAAT
1 ATATATAAAT
56384771 ATATATAAAT
1 ATATATAAAT
56384781 ATATATAA
1 ATATATAA
56384789 TAAATTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
ATATATAAAT
Found at i:56387044 original size:24 final size:24
Alignment explanation
Indices: 56387017--56387068 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
56387007 ACCAAAAATA
56387017 TTCAAAGACTTGACATGTAAATTT
1 TTCAAAGACTTGACATGTAAATTT
** *
56387041 TTCATTGACTTGATATGTAAATTT
1 TTCAAAGACTTGACATGTAAATTT
56387065 TTCA
1 TTCA
56387069 TTTTGATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.44
Consensus pattern (24 bp):
TTCAAAGACTTGACATGTAAATTT
Found at i:56387069 original size:24 final size:24
Alignment explanation
Indices: 56387023--56387070 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
56387013 AATATTCAAA
56387023 GACTTGACATGTAAATTTTTCATT
1 GACTTGACATGTAAATTTTTCATT
*
56387047 GACTTGATATGTAAATTTTTCATT
1 GACTTGACATGTAAATTTTTCATT
56387071 TTGATTAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.48
Consensus pattern (24 bp):
GACTTGACATGTAAATTTTTCATT
Found at i:56391854 original size:14 final size:14
Alignment explanation
Indices: 56391829--56391866 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
56391819 TAACATTATG
56391829 TTAAAA-ATTAAAA
1 TTAAAATATTAAAA
56391842 TTAAAATATTAAAA
1 TTAAAATATTAAAA
*
56391856 TTTAAAT-TTAA
1 TTAAAATATTAA
56391867 GCTGAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TTAAAATATTAAAA
Found at i:56393688 original size:20 final size:19
Alignment explanation
Indices: 56393643--56393688 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
56393633 TTCCAAACTT
*
56393643 GAGTTGTTCTCAATATAAA
1 GAGTTGTTCTAAATATAAA
*
56393662 G-GTTGTTCTAAATAATTAA
1 GAGTTGTTCTAAAT-ATAAA
56393681 GAGTTGTT
1 GAGTTGTT
56393689 TTGTGGTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 11 0.48
19 6 0.26
20 6 0.26
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.41
Consensus pattern (19 bp):
GAGTTGTTCTAAATATAAA
Found at i:56396419 original size:31 final size:31
Alignment explanation
Indices: 56396361--56396439 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
56396351 TTATTGTACT
* * *
56396361 ATTTGGTTCCTATA-TTTGACTTGAATGTTTA
1 ATTTGGTACCTA-AGTTTGACTTCAATGTTCA
* *
56396392 ATTTGGTACCTGAGTTTGGCTTCAATGTTCA
1 ATTTGGTACCTAAGTTTGACTTCAATGTTCA
*
56396423 ATTTGGTGCCTAAGTTT
1 ATTTGGTACCTAAGTTT
56396440 TTTCAAATTG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
30 1 0.03
31 39 0.98
ACGTcount: A:0.20, C:0.13, G:0.20, T:0.47
Consensus pattern (31 bp):
ATTTGGTACCTAAGTTTGACTTCAATGTTCA
Found at i:56401500 original size:24 final size:24
Alignment explanation
Indices: 56401455--56401500 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
56401445 AACACGTGTG
* *
56401455 TATGTACTATCCATTTTGAATTTA
1 TATGTACTATCCAATTTAAATTTA
**
56401479 TATGTACTATGTAATTTAAATT
1 TATGTACTATCCAATTTAAATT
56401501 GTCTCCTATG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.50
Consensus pattern (24 bp):
TATGTACTATCCAATTTAAATTTA
Found at i:56403032 original size:20 final size:18
Alignment explanation
Indices: 56402982--56403040 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
56402972 GTAAAAATCG
56402982 TAAAAATTGT-AAAATATA
1 TAAAAA-TGTAAAAATATA
* *
56403000 TAGAACTGTAAAAATATA
1 TAAAAATGTAAAAATATA
*
56403018 TAAAAATGTAAAAAAATA
1 TAAAAATGTAAAAATATA
56403036 TAAAA
1 TAAAA
56403041 TTATTCCCAC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
17 3 0.09
18 32 0.91
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.27
Consensus pattern (18 bp):
TAAAAATGTAAAAATATA
Found at i:56403129 original size:19 final size:19
Alignment explanation
Indices: 56403078--56403133 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
56403068 TTATAAAGTA
56403078 GTAAGAAAATTATAAAAAAT
1 GTAA-AAAATTATAAAAAAT
* **
56403098 G-AAAAGAAATATAAAATTT
1 GTAAAA-AATTATAAAAAAT
56403117 GTAAAAAATTATAAAAA
1 GTAAAAAATTATAAAAA
56403134 TTATCGTACC
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
18 2 0.07
19 22 0.76
20 5 0.17
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.25
Consensus pattern (19 bp):
GTAAAAAATTATAAAAAAT
Found at i:56403362 original size:20 final size:20
Alignment explanation
Indices: 56403337--56403379 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
56403327 TTTATAAAAG
56403337 TTTACAATCTTTATAATTTT
1 TTTACAATCTTTATAATTTT
*
56403357 TTTACAATTTTTATAATTTT
1 TTTACAATCTTTATAATTTT
56403377 TTT
1 TTT
56403380 GTCACACGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTACAATCTTTATAATTTT
Found at i:56406011 original size:38 final size:37
Alignment explanation
Indices: 56405928--56406013 Score: 113
Period size: 38 Copynumber: 2.3 Consensus size: 37
56405918 CTCTGTACAA
56405928 CCTGTAGATAATCATTTCATGGTGTCGCTTCGTAAAG
1 CCTGTAGATAATCATTTCATGGTGTCGCTTCGTAAAG
* *
56405965 CTTATAGATAATCATTTTCATGGTGTCGC-TC-TATAGAG
1 CCTGTAGATAATCA-TTTCATGGTGTCGCTTCGTA-A-AG
56406003 CCTGTAGATAA
1 CCTGTAGATAA
56406014 CCATACCACG
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
36 2 0.05
37 15 0.36
38 25 0.60
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (37 bp):
CCTGTAGATAATCATTTCATGGTGTCGCTTCGTAAAG
Found at i:56407883 original size:41 final size:41
Alignment explanation
Indices: 56407838--56407994 Score: 242
Period size: 41 Copynumber: 3.8 Consensus size: 41
56407828 TTGTATATAA
** * * *
56407838 CACCGGCATAAAGCCTGCTAGGCACCAAGCCCGATACATTT
1 CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGATATAATT
* * *
56407879 CACCGGCACAAAGCCTGCTAGACATAAAGTCTGATATAATT
1 CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGATATAATT
56407920 CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGATATAATT
1 CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGATATAATT
56407961 CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGA
1 CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGA
56407995 ACTTACAAAA
Statistics
Matches: 105, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 105 1.00
ACGTcount: A:0.33, C:0.28, G:0.20, T:0.19
Consensus pattern (41 bp):
CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGATATAATT
Found at i:56409138 original size:16 final size:17
Alignment explanation
Indices: 56409117--56409148 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
56409107 AAATATGCAA
56409117 TCACATAA-TTCATATT
1 TCACATAACTTCATATT
56409133 TCACATAACTTCATAT
1 TCACATAACTTCATAT
56409149 CATCAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (17 bp):
TCACATAACTTCATATT
Found at i:56409398 original size:41 final size:41
Alignment explanation
Indices: 56409310--56409464 Score: 154
Period size: 41 Copynumber: 3.7 Consensus size: 41
56409300 GGCTCGTACA
** * *
56409310 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATG
1 ATGCCAACGTCCCAGACGTGGTCTTACA-CAAATCAAATACG
56409352 ATGCC-ACTGTCCCAGACAG-GGTCTTACACAAATCAAATACG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACAAATCAAATACG
* * * **
56409393 ATGCCAATGTCCCGGACATGGTCTTACACGTATACACAAGT-CG
1 ATGCCAACGTCCCAGACGTGGTCTTACACAAAT-CA-AA-TACG
56409436 ATGCCAACGTCCCAGACGTGGTCTTACAC
1 ATGCCAACGTCCCAGACGTGGTCTTACAC
56409465 GAAAATACAT
Statistics
Matches: 94, Mismatches: 12, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
41 36 0.38
42 26 0.28
43 31 0.33
44 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (41 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACAAATCAAATACG
Found at i:56410310 original size:28 final size:31
Alignment explanation
Indices: 56410278--56410336 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 31
56410268 CCTTTCCTTT
56410278 TTATTATAATAAC-ATTAT-AATA-TATAAA
1 TTATTATAATAACTATTATAAATAGTATAAA
* *
56410306 TTATTATTATAACTTTTATAAATAGTATAAA
1 TTATTATAATAACTATTATAAATAGTATAAA
56410337 AACTATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 12 0.46
29 4 0.15
30 4 0.15
31 6 0.23
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (31 bp):
TTATTATAATAACTATTATAAATAGTATAAA
Found at i:56419561 original size:23 final size:21
Alignment explanation
Indices: 56419526--56419593 Score: 57
Period size: 24 Copynumber: 3.0 Consensus size: 21
56419516 ATCTTTATAT
56419526 TCTC-TTATATTTTAAATTTAA
1 TCTCTTTAT-TTTTAAATTTAA
*
56419547 TCTCTATTTATTTTTAAGAATTTAG
1 TCTC--TTTATTTTT-A-AATTTAA
*
56419572 TCTCTTTATTTTTTGAATTTAA
1 TCTCTTTA-TTTTTAAATTTAA
56419594 AAATTTAGGT
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
21 4 0.11
22 6 0.16
23 8 0.21
24 10 0.26
25 10 0.26
ACGTcount: A:0.28, C:0.09, G:0.04, T:0.59
Consensus pattern (21 bp):
TCTCTTTATTTTTAAATTTAA
Found at i:56419570 original size:25 final size:22
Alignment explanation
Indices: 56419526--56419593 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 22
56419516 ATCTTTATAT
56419526 TCTC-TTATATTTTA-AATTTAA
1 TCTCTTTAT-TTTTAGAATTTAA
*
56419547 TCTCTATTTATTTTTAAGAATTTAG
1 TCTC--TTTATTTTT-AGAATTTAA
*
56419572 TCTCTTTATTTTTTGAATTTAA
1 TCTCTTTATTTTTAGAATTTAA
56419594 AAATTTAGGT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
21 4 0.10
22 7 0.18
23 13 0.33
24 5 0.13
25 10 0.26
ACGTcount: A:0.28, C:0.09, G:0.04, T:0.59
Consensus pattern (22 bp):
TCTCTTTATTTTTAGAATTTAA
Found at i:56419589 original size:22 final size:22
Alignment explanation
Indices: 56419526--56419593 Score: 66
Period size: 25 Copynumber: 3.0 Consensus size: 22
56419516 ATCTTTATAT
* *
56419526 TCTC-TTATATTTTAAATTTAA
1 TCTCTTTATTTTTTGAATTTAA
* *
56419547 TCTCTATTTATTTTTAAGAATTTAG
1 TCTC--TTTATTTTT-TGAATTTAA
56419572 TCTCTTTATTTTTTGAATTTAA
1 TCTCTTTATTTTTTGAATTTAA
56419594 AAATTTAGGT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
21 4 0.11
22 7 0.19
23 9 0.24
24 7 0.19
25 10 0.27
ACGTcount: A:0.28, C:0.09, G:0.04, T:0.59
Consensus pattern (22 bp):
TCTCTTTATTTTTTGAATTTAA
Found at i:56425137 original size:120 final size:120
Alignment explanation
Indices: 56424980--56425610 Score: 1016
Period size: 120 Copynumber: 5.2 Consensus size: 120
56424970 TATATTTAGA
* * * * *
56424980 AAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGT
1 AAAA-TATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGT
*
56425045 AAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATCATATATTTTAATT
65 AAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATATTTTAATT
* * * *
56425101 AAAATATATTTAATAATAATTAT-TTCAAATTATATTTTATAGTATCATATATTATAATTTTAGT
1 AAAATATATTTAATAATAATTATGTT-AATTTATATTTTACAGTATCATATATTATGATTTGAGT
* * *
56425165 AAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATCATATATTTTAATT
65 AAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATATTTTAATT
56425221 AAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTA
1 AAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTA
* *
56425286 AATTAATATAAGAATA-TTAATTATTAAGAATTTTATTAAATTATATAGTTTAATT
66 AATTCATATAAGAATATTTAA-TATTAAGAATTTTATTAAATTATATATTTTAATT
*
56425341 AAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTA
1 AAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTA
*
56425406 AATTAATATAAGAATA-TTAATTATTAAGAATTTTATTAAATTATATATTTTAATT
66 AATTCATATAAGAATATTTAA-TATTAAGAATTTTATTAAATTATATATTTTAATT
56425461 AAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTA
1 AAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTA
* *
56425526 AATTCATATAAGAATATTGATTATTAAGAATTTTATTATAAATTATATATTTTAATT
66 AATTCATATAAGAATATTTAATATTAAGAATTTTA-T-TAAATTATATATTTTAATT
56425583 AAAATATATTTAATAATAATTATGTTAA
1 AAAATATATTTAATAATAATTATGTTAA
56425611 AATATGATTA
Statistics
Matches: 485, Mismatches: 19, Indels: 11
0.94 0.04 0.02
Matches are distributed among these distances:
119 4 0.01
120 425 0.88
121 9 0.02
122 47 0.10
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.48
Consensus pattern (120 bp):
AAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTA
AATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATATTTTAATT
Found at i:56425463 original size:18 final size:17
Alignment explanation
Indices: 56425435--56425469 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
56425425 ATTATTAAGA
*
56425435 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
56425452 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
56425470 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:56425590 original size:18 final size:19
Alignment explanation
Indices: 56425555--56425591 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
56425545 ATTATTAAGA
56425555 ATTTTATTATAAATTATAT
1 ATTTTATTATAAATTATAT
56425574 ATTTTAATTA-AAA-TATAT
1 ATTTT-ATTATAAATTATAT
56425592 TTAATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.29
19 8 0.47
20 4 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTTTATTATAAATTATAT
Found at i:56425878 original size:16 final size:17
Alignment explanation
Indices: 56425827--56425896 Score: 126
Period size: 17 Copynumber: 4.2 Consensus size: 17
56425817 TATTAGCTAT
56425827 TACACCTCTAATCCCAA
1 TACACCTCTAATCCCAA
56425844 TACACCTCTAATCCCAA
1 TACACCTCTAATCCCAA
56425861 TACACCTCTAAT-CCAA
1 TACACCTCTAATCCCAA
56425877 TACACCTCTAAT-CCAA
1 TACACCTCTAATCCCAA
56425893 TACA
1 TACA
56425897 GCGAACCAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
16 24 0.45
17 29 0.55
ACGTcount: A:0.37, C:0.39, G:0.00, T:0.24
Consensus pattern (17 bp):
TACACCTCTAATCCCAA
Found at i:56425882 original size:33 final size:33
Alignment explanation
Indices: 56425827--56425896 Score: 124
Period size: 33 Copynumber: 2.1 Consensus size: 33
56425817 TATTAGCTAT
56425827 TACACCTCTAATCCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCCAATACACCTCTAAT-CCAA
56425861 TACACCTCTAAT-CCAATACACCTCTAATCCAA
1 TACACCTCTAATCCCAATACACCTCTAATCCAA
56425893 TACA
1 TACA
56425897 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
32 8 0.22
33 16 0.44
34 12 0.33
ACGTcount: A:0.37, C:0.39, G:0.00, T:0.24
Consensus pattern (33 bp):
TACACCTCTAATCCCAATACACCTCTAATCCAA
Found at i:56433681 original size:21 final size:20
Alignment explanation
Indices: 56433657--56433702 Score: 51
Period size: 19 Copynumber: 2.3 Consensus size: 20
56433647 GTAAGTTACC
56433657 ATGAAGAATTTATAGAATT-TT
1 ATGAAGAA-TTATA-AATTATT
*
56433678 ATGATGAATTATAAATTATT
1 ATGAAGAATTATAAATTATT
56433698 -TGAAG
1 ATGAAG
56433703 CTTTAATTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 8 0.36
20 7 0.32
21 7 0.32
ACGTcount: A:0.43, C:0.00, G:0.15, T:0.41
Consensus pattern (20 bp):
ATGAAGAATTATAAATTATT
Found at i:56435513 original size:45 final size:45
Alignment explanation
Indices: 56435416--56435518 Score: 163
Period size: 46 Copynumber: 2.3 Consensus size: 45
56435406 TAATTTTGTA
*
56435416 AAGAAAACCATACTAAGTTGTGAAATGTAGGTATGGTATTTCAGT
1 AAGAAAACCATACTAAGTTGTGAAAAGTAGGTATGGTATTTCAGT
*
56435461 AATGAAAATCATACTAAGTTGTGAAAAGTAGGT-TGGTATTTCAGT
1 AA-GAAAACCATACTAAGTTGTGAAAAGTAGGTATGGTATTTCAGT
56435506 GAAGAAAACCATA
1 -AAGAAAACCATA
56435519 TTGAGTTATA
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
45 23 0.43
46 30 0.57
ACGTcount: A:0.41, C:0.09, G:0.21, T:0.29
Consensus pattern (45 bp):
AAGAAAACCATACTAAGTTGTGAAAAGTAGGTATGGTATTTCAGT
Found at i:56436320 original size:92 final size:91
Alignment explanation
Indices: 56436204--56436426 Score: 227
Period size: 91 Copynumber: 2.5 Consensus size: 91
56436194 AAAAGTTTTT
* ** * * * *
56436204 AAACTGTTTCAAAAAAAAGTAATTAAGTCTATGT-TTTTTTTTTTTGCA-TTCAATTGGGTACTT
1 AAACTTTTTCAAAAAAAAACAATTAAG-CT-TCTACTTTTTTTTTGGCACTT-AATTAGGTACTT
** * *
56436267 AATTTTCAAAATGCATCAAAAAGGACTTC
63 AAGCTGCAAAATGCATCAAAAAGGACGTC
* *
56436296 AAATTTTTTCAAAAAAAAACAATTAAGCTTCTACTTTTTTTTTGGCACTTAATTAGGTACTTGAG
1 AAACTTTTTCAAAAAAAAACAATTAAGCTTCTACTTTTTTTTTGGCACTTAATTAGGTACTTAAG
* *
56436361 CTGCAAAATGCATGAAAAAGGCCGTC
66 CTGCAAAATGCATCAAAAAGGACGTC
* * * *
56436387 GAACTTTTTC-AAAAAAACCAATTAAGCTCCAACTTTTTTT
1 AAACTTTTTCAAAAAAAAACAATTAAGCTTCTACTTTTTTT
56436427 CTCACTCAAT
Statistics
Matches: 109, Mismatches: 20, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
90 29 0.27
91 55 0.50
92 25 0.23
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (91 bp):
AAACTTTTTCAAAAAAAAACAATTAAGCTTCTACTTTTTTTTTGGCACTTAATTAGGTACTTAAG
CTGCAAAATGCATCAAAAAGGACGTC
Found at i:56436424 original size:90 final size:89
Alignment explanation
Indices: 56436273--56436447 Score: 226
Period size: 90 Copynumber: 2.0 Consensus size: 89
56436263 ACTTAATTTT
* * * * *
56436273 CAAAATGCATCAAAAAGGACTTCAAATTTTTTCAAAAAAAAACAATTAAGCTTCTACTTTTTTTT
1 CAAAATGCATCAAAAAGGACGTCAAACTTTTTCAAAAAAAAACAATTAAGCTCCAACTTTTTTTC
*
56436338 TGGCACTTAATTAGGTACTTGAGCTG
66 T--CACTCAATTAGGTACTTGAGCTG
* * * *
56436364 CAAAATGCATGAAAAAGGCCGTCGAACTTTTTC-AAAAAAACCAATTAAGCTCCAACTTTTTTTC
1 CAAAATGCATCAAAAAGGACGTCAAACTTTTTCAAAAAAAAACAATTAAGCTCCAACTTTTTTTC
*
56436428 TCACTCAATTGGGTACTTGA
66 TCACTCAATTAGGTACTTGA
56436448 ACTACCAGAA
Statistics
Matches: 73, Mismatches: 11, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
88 17 0.23
90 28 0.38
91 28 0.38
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.33
Consensus pattern (89 bp):
CAAAATGCATCAAAAAGGACGTCAAACTTTTTCAAAAAAAAACAATTAAGCTCCAACTTTTTTTC
TCACTCAATTAGGTACTTGAGCTG
Found at i:56436467 original size:88 final size:90
Alignment explanation
Indices: 56436240--56436468 Score: 223
Period size: 91 Copynumber: 2.6 Consensus size: 90
56436230 GTCTATGTTT
* * * * * * * * * *
56436240 TTTTTTTTTGCATTCAATTGGGTACTT-AATTTTCAAAATGCATCAAAAAGGACTTCAAATTTTT
1 TTTTTTTCTGCACTCAATTAGGTACTTGAA-CTCCAAAATGCATAAAAAAGGCCGTCGAACTTTT
* *
56436304 TCAAAAAAAAACAATTAAGCTTCTAC
65 TCAAAAAAAAACAATTAAGCTCCAAC
* * * * *
56436330 TTTTTTTTTGGCACTTAATTAGGTACTTGAGCTGCAAAATGCATGAAAAAGGCCGTCGAACTTTT
1 TTTTTTTCT-GCACTCAATTAGGTACTTGAACTCCAAAATGCATAAAAAAGGCCGTCGAACTTTT
*
56436395 TC-AAAAAAACCAATTAAGCTCCAAC
65 TCAAAAAAAAACAATTAAGCTCCAAC
* *
56436420 TTTTTTTCT-CACTCAATTGGGTACTTGAACTACCAGAAT-CATAAAAAAG
1 TTTTTTTCTGCACTCAATTAGGTACTTGAACT-CCAAAATGCATAAAAAAG
56436469 ACCCTCAAAC
Statistics
Matches: 115, Mismatches: 21, Indels: 8
0.80 0.15 0.06
Matches are distributed among these distances:
88 28 0.24
89 5 0.04
90 37 0.32
91 44 0.38
92 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (90 bp):
TTTTTTTCTGCACTCAATTAGGTACTTGAACTCCAAAATGCATAAAAAAGGCCGTCGAACTTTTT
CAAAAAAAAACAATTAAGCTCCAAC
Found at i:56436480 original size:88 final size:90
Alignment explanation
Indices: 56436240--56436480 Score: 222
Period size: 90 Copynumber: 2.7 Consensus size: 90
56436230 GTCTATGTTT
* * * * * * * *
56436240 TTTTTTTTTGCATTCAATTGGGTACTT-AATTTTCAAAATGCATCAAAAAGGA-CTTCAAATTTT
1 TTTTTTTCTGCACTCAATTAGGTACTTGAA-CTCCAAAATGCAT-AAAAAAGACCCTCAAACTTT
* *
56436303 TTCAAAAAAAAACAATTAAGCTTCTAC
64 TTCAAAAAAAAACAATTAAGCTCCAAC
* * * * * * * *
56436330 TTTTTTTTTGGCACTTAATTAGGTACTTGAGCTGCAAAATGCATGAAAAAGGCCGTCGAACTTTT
1 TTTTTTTCT-GCACTCAATTAGGTACTTGAACTCCAAAATGCATAAAAAAGACCCTCAAACTTTT
*
56436395 TC-AAAAAAACCAATTAAGCTCCAAC
65 TCAAAAAAAAACAATTAAGCTCCAAC
* *
56436420 TTTTTTTCT-CACTCAATTGGGTACTTGAACTACCAGAAT-CATAAAAAAGACCCTCAAACTT
1 TTTTTTTCTGCACTCAATTAGGTACTTGAACT-CCAAAATGCATAAAAAAGACCCTCAAACTT
56436481 AAAAAAAGAA
Statistics
Matches: 122, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
88 37 0.30
89 5 0.04
90 42 0.34
91 37 0.30
92 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (90 bp):
TTTTTTTCTGCACTCAATTAGGTACTTGAACTCCAAAATGCATAAAAAAGACCCTCAAACTTTTT
CAAAAAAAAACAATTAAGCTCCAAC
Found at i:56436696 original size:19 final size:19
Alignment explanation
Indices: 56436674--56436759 Score: 95
Period size: 19 Copynumber: 4.4 Consensus size: 19
56436664 ATTATAAAAA
56436674 ATAAAAATGAATAAAATTT
1 ATAAAAATGAATAAAATTT
*
56436693 ATAAAAATGAATAAATTTT
1 ATAAAAATGAATAAAATTT
*
56436712 AATAAAAAT-ATTTAAAATTT
1 -ATAAAAATGA-ATAAAATTT
*
56436732 ATTAAAAATAGAATAAAA-CT
1 A-TAAAAAT-GAATAAAATTT
56436752 ATAAAAAT
1 ATAAAAAT
56436760 TGTAAAATAT
Statistics
Matches: 57, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
19 27 0.47
20 24 0.42
21 5 0.09
22 1 0.02
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (19 bp):
ATAAAAATGAATAAAATTT
Found at i:56436716 original size:20 final size:20
Alignment explanation
Indices: 56436673--56436749 Score: 95
Period size: 20 Copynumber: 3.9 Consensus size: 20
56436663 AATTATAAAA
56436673 AATAAAAATGAATAAAATTT
1 AATAAAAATGAATAAAATTT
*
56436693 -ATAAAAATGAATAAATTTT
1 AATAAAAATGAATAAAATTT
*
56436712 AATAAAAAT-ATTTAAAATTT
1 AATAAAAATGA-ATAAAATTT
*
56436732 ATTAAAAATAGAATAAAA
1 AATAAAAAT-GAATAAAA
56436750 CTATAAAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
19 19 0.40
20 23 0.48
21 5 0.10
22 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (20 bp):
AATAAAAATGAATAAAATTT
Found at i:56436756 original size:39 final size:38
Alignment explanation
Indices: 56436685--56436772 Score: 99
Period size: 39 Copynumber: 2.3 Consensus size: 38
56436675 TAAAAATGAA
** *
56436685 TAAAATTTATAAAAATGAATAAATTTTAATAAAAATATT
1 TAAAATTTATAAAAATGAATAAATACTAATAAAAAT-TG
56436724 TAAAATTTATTAAAAATAGAATAAA-ACT-ATAAAAATTG
1 TAAAATTTA-TAAAAAT-GAATAAATACTAATAAAAATTG
*
56436762 TAAAATATATA
1 TAAAATTTATA
56436773 GAACTATAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
37 2 0.05
38 9 0.21
39 17 0.40
40 8 0.19
41 7 0.16
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.35
Consensus pattern (38 bp):
TAAAATTTATAAAAATGAATAAATACTAATAAAAATTG
Found at i:56436772 original size:18 final size:18
Alignment explanation
Indices: 56436751--56436807 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
56436741 AGAATAAAAC
56436751 TATAAAAATTGTAAAATA
1 TATAAAAATTGTAAAATA
* * *
56436769 TATAGAACTAT-AAAAATA
1 TATAAAAAT-TGTAAAATA
*
56436787 TATAAAAA-TGTAAAAAA
1 TATAAAAATTGTAAAATA
56436804 TATA
1 TATA
56436808 TATAAAATTA
Statistics
Matches: 30, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
16 1 0.03
17 9 0.30
18 19 0.63
19 1 0.03
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (18 bp):
TATAAAAATTGTAAAATA
Found at i:56436790 original size:10 final size:10
Alignment explanation
Indices: 56436777--56436815 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
56436767 TATATAGAAC
56436777 TATAAAAATA
1 TATAAAAATA
*
56436787 TATAAAAATG
1 TATAAAAATA
56436797 TA-AAAAATA
1 TATAAAAATA
56436806 TATATAAAAT
1 TATA-AAAAT
56436816 TATTCCCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 8 0.32
10 12 0.48
11 5 0.20
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (10 bp):
TATAAAAATA
Found at i:56436804 original size:19 final size:19
Alignment explanation
Indices: 56436674--56436815 Score: 64
Period size: 19 Copynumber: 7.4 Consensus size: 19
56436664 ATTATAAAAA
*
56436674 ATAAAAATG-AATAAAATTT
1 ATAAAAATGTAA-AAAATAT
* *
56436693 ATAAAAATG-AATAAATTTT
1 ATAAAAATGTAA-AAAATAT
* ** *
56436712 AATAAAAATATTTAAAATTT
1 -ATAAAAATGTAAAAAATAT
56436732 ATTAAAAATAG-AATAAAACTAT
1 A-TAAAAAT-GTAA-AAAA-TAT
*
56436754 A-AAAATTGT--AAAATAT
1 ATAAAAATGTAAAAAATAT
* * *
56436770 ATAGAACTAT-AAAAATAT
1 ATAAAAATGTAAAAAATAT
56436788 ATAAAAATGTAAAAAATAT
1 ATAAAAATGTAAAAAATAT
56436807 ATATAAAAT
1 ATA-AAAAT
56436816 TATTCCCAAA
Statistics
Matches: 96, Mismatches: 16, Indels: 21
0.72 0.12 0.16
Matches are distributed among these distances:
16 4 0.04
17 9 0.09
18 14 0.15
19 31 0.32
20 31 0.32
21 4 0.04
22 3 0.03
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.32
Consensus pattern (19 bp):
ATAAAAATGTAAAAAATAT
Found at i:56436882 original size:19 final size:20
Alignment explanation
Indices: 56436850--56436906 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 20
56436840 TTATAAAGTA
*
56436850 GTAAGAAAATTATAAAAAAT
1 GTAAAAAAATTATAAAAAAT
* **
56436870 GTAAAGAAA-TATAAAATTT
1 GTAAAAAAATTATAAAAAAT
56436889 GTAAAAAAATTATAAAAA
1 GTAAAAAAATTATAAAAA
56436907 TTATCTTACC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (20 bp):
GTAAAAAAATTATAAAAAAT
Found at i:56437151 original size:20 final size:20
Alignment explanation
Indices: 56437109--56437149 Score: 68
Period size: 18 Copynumber: 2.1 Consensus size: 20
56437099 TTTATAAAAG
56437109 TTTACAATCTTTATAATTTT
1 TTTACAATCTTTATAATTTT
56437129 TTTACAAT-TTTAT-ATTTT
1 TTTACAATCTTTATAATTTT
56437147 TTT
1 TTT
56437150 TTTCTCACAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 8 0.38
19 5 0.24
20 8 0.38
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTACAATCTTTATAATTTT
Found at i:56441077 original size:38 final size:38
Alignment explanation
Indices: 56441020--56441123 Score: 127
Period size: 38 Copynumber: 2.7 Consensus size: 38
56441010 TTTTGAAGTA
* * * * *
56441020 TCGCTCTATACAGCTTGTAGATAATCATTTTTATGGTG
1 TCGCTCCATAGAGCCTGTAGATAACCATTTTCATGGTG
* *
56441058 TCGCTTCGTAGAGCCTGTAGATAACCATTTTCATGGTG
1 TCGCTCCATAGAGCCTGTAGATAACCATTTTCATGGTG
**
56441096 TCGCTCCATAGAGCCCATAGATAACCAT
1 TCGCTCCATAGAGCCTGTAGATAACCAT
56441124 ACCACAATGC
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 55 1.00
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (38 bp):
TCGCTCCATAGAGCCTGTAGATAACCATTTTCATGGTG
Found at i:56444754 original size:43 final size:43
Alignment explanation
Indices: 56444675--56444796 Score: 142
Period size: 43 Copynumber: 2.9 Consensus size: 43
56444665 CAATAGCCTC
*
56444675 TGATCTGTAGCGGCGCTTTCT-CACAAACG-CGACTAAAGACCA
1 TGATCTTTAGCGGCGCTTTCTCCACAAACGCCG-CTAAAGACCA
* * *
56444717 TGATCTTTAGTGGCGCTTTTTCCACAAACGCCGCTAAAGACCC
1 TGATCTTTAGCGGCGCTTTCTCCACAAACGCCGCTAAAGACCA
* ** *
56444760 TTATCTTTAGCGGCGCTTTGACCA-AAACGCCACTAAA
1 TGATCTTTAGCGGCGCTTTCTCCACAAACGCCGCTAAA
56444797 TTTGGCAGAT
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
42 30 0.43
43 37 0.54
44 2 0.03
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (43 bp):
TGATCTTTAGCGGCGCTTTCTCCACAAACGCCGCTAAAGACCA
Found at i:56445148 original size:21 final size:21
Alignment explanation
Indices: 56445106--56445197 Score: 78
Period size: 21 Copynumber: 4.4 Consensus size: 21
56445096 TTTGACGCTG
**
56445106 CTCTGCTTCCCTCGCTTTAGC
1 CTCTGCTTCCCTCGCTGCAGC
56445127 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* * * *
56445148 CTGTACTTCTCTCACTGCCA-C
1 CTCTGCTTCCCTCGCTG-CAGC
* * *
56445169 CTCTGCTTCTCTTGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
*
56445190 ATCTGCTT
1 CTCTGCTT
56445198 TAAGCTGCTG
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
20 1 0.02
21 54 0.95
22 2 0.04
ACGTcount: A:0.07, C:0.42, G:0.15, T:0.36
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:56445243 original size:66 final size:66
Alignment explanation
Indices: 56445167--56445312 Score: 197
Period size: 66 Copynumber: 2.2 Consensus size: 66
56445157 TCTCACTGCC
* *
56445167 ACCTCTGCTTCTCTTGCTGCCGCATCTGCTTTAAGCTGCT-GCTGGAGCTCTTCATA-CTTTCGT
1 ACCTCAGCTTCTCTTGCTGCCGCATCTACTTTAAGCTG-TAGCTGGAGCTCTTCATATCTTT-GT
56445230 TGA
64 TGA
* * * * *
56445233 ACCTCAGCTTCTCTTGCTGCTGCATCTACTTTCAGTTGTAGCTGGAGTTCTTCATATCTTTTTTG
1 ACCTCAGCTTCTCTTGCTGCCGCATCTACTTTAAGCTGTAGCTGGAGCTCTTCATATCTTTGTTG
56445298 A
66 A
56445299 ACCTCAGCTTCTCT
1 ACCTCAGCTTCTCT
56445313 CGATGTTGCC
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
65 1 0.01
66 66 0.93
67 4 0.06
ACGTcount: A:0.14, C:0.29, G:0.17, T:0.40
Consensus pattern (66 bp):
ACCTCAGCTTCTCTTGCTGCCGCATCTACTTTAAGCTGTAGCTGGAGCTCTTCATATCTTTGTTG
A
Found at i:56445336 original size:66 final size:65
Alignment explanation
Indices: 56445167--56445338 Score: 175
Period size: 66 Copynumber: 2.6 Consensus size: 65
56445157 TCTCACTGCC
* * * * * *
56445167 ACCTCTGCTTCTCTTGCTGCCGCATCTGCTTTAAGCTGCTGCTGGAGCTCTTCATACTTTCGTTG
1 ACCTCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTG-TGCTGGAGCTCTTCATACTTTCGTTG
56445232 A
65 A
* * ** * * *
56445233 ACCTCAGCTTCTCTTGCTGCTGCATCTACTTTCAGTTGTAGCTGGAGTTCTTCATATCTTT-TTT
1 ACCTCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTGT-GCTGGAGCTCTTCATA-CTTTCGTT
56445297 GA
64 GA
* *
56445299 ACCTCAGCTTCTCTCGATGTTGCCTCCGCTTTAAGTTGTG
1 ACCTCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTGTG
56445339 TAATTTGCTC
Statistics
Matches: 90, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
65 2 0.02
66 84 0.93
67 4 0.04
ACGTcount: A:0.13, C:0.28, G:0.19, T:0.40
Consensus pattern (65 bp):
ACCTCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTGTGCTGGAGCTCTTCATACTTTCGTTGA
Found at i:56446866 original size:14 final size:17
Alignment explanation
Indices: 56446835--56446871 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 17
56446825 ATTATAAAGG
56446835 ATATTATTAAATTAATT
1 ATATTATTAAATTAATT
56446852 ATATTA-TAAA-T-ATT
1 ATATTATTAAATTAATT
56446866 ATATTA
1 ATATTA
56446872 AGAAATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 9 0.45
15 1 0.05
16 4 0.20
17 6 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATTATTAAATTAATT
Found at i:56447047 original size:14 final size:14
Alignment explanation
Indices: 56447021--56447071 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
56447011 GAAAACAAAA
56447021 GAAATAAAATAAAG
1 GAAATAAAATAAAG
*
56447035 GAAATAAAGTAAAG
1 GAAATAAAATAAAG
* * *
56447049 TAAGTTAAAATAAAA
1 GAA-ATAAAATAAAG
56447064 G-AATAAAA
1 GAAATAAAA
56447072 GAAACAAAAG
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
13 5 0.17
14 16 0.55
15 8 0.28
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.18
Consensus pattern (14 bp):
GAAATAAAATAAAG
Found at i:56447082 original size:17 final size:16
Alignment explanation
Indices: 56447060--56447093 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
56447050 AAGTTAAAAT
56447060 AAAAGAATAAAAGAAAC
1 AAAAGAA-AAAAGAAAC
*
56447077 AAAAGAAGAAAGAAAC
1 AAAAGAAAAAAGAAAC
56447093 A
1 A
56447094 GAATAGCCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.76, C:0.06, G:0.15, T:0.03
Consensus pattern (16 bp):
AAAAGAAAAAAGAAAC
Found at i:56447810 original size:18 final size:18
Alignment explanation
Indices: 56447787--56447835 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
56447777 ATGTGAGGTA
*
56447787 AGTATTAATATTAGTATT
1 AGTATTATTATTAGTATT
56447805 AGTATTATTATTAGTATT
1 AGTATTATTATTAGTATT
*
56447823 ATTATTATTATTA
1 AGTATTATTATTA
56447836 TGAGTGGGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (18 bp):
AGTATTATTATTAGTATT
Found at i:56447815 original size:3 final size:3
Alignment explanation
Indices: 56447789--56447836 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
56447779 GTGAGGTAAG
* * * *
56447789 TAT TAA TAT TAG TAT TAG TAT TAT TAT TAG TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
56447837 GAGTGGGAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:56447836 original size:12 final size:12
Alignment explanation
Indices: 56447789--56447836 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
56447779 GTGAGGTAAG
* *
56447789 TATTAATATTAG
1 TATTAGTATTAT
56447801 TATTAGTATTAT
1 TATTAGTATTAT
56447813 TATTAGTATTAT
1 TATTAGTATTAT
*
56447825 TATTATTATTAT
1 TATTAGTATTAT
56447837 GAGTGGGAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (12 bp):
TATTAGTATTAT
Found at i:56448031 original size:24 final size:24
Alignment explanation
Indices: 56447977--56448047 Score: 65
Period size: 24 Copynumber: 2.9 Consensus size: 24
56447967 TGTGTGAAGT
*
56447977 TGTGAAATAATTATTG-ATTG-AAA
1 TGTGAAA-AATGATTGAATTGAAAA
*
56448000 GGTGGAAAAATGATTGAATTGAAAA
1 TGT-GAAAAATGATTGAATTGAAAA
*
56448025 TGTGAAAATTGTAATTGAATTGA
1 TGTGAAAAATG--ATTGAATTGA
56448048 GAATATATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
23 9 0.23
24 15 0.38
25 5 0.13
26 10 0.26
ACGTcount: A:0.44, C:0.00, G:0.23, T:0.34
Consensus pattern (24 bp):
TGTGAAAAATGATTGAATTGAAAA
Found at i:56448250 original size:37 final size:39
Alignment explanation
Indices: 56448191--56448286 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
56448181 CGGATAGATT
* * * *
56448191 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
56448228 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
56448267 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
56448287 TTCTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 24 0.50
40 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Found at i:56454327 original size:14 final size:17
Alignment explanation
Indices: 56454296--56454332 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 17
56454286 ATTATAAAGG
56454296 ATATTATTAAATTAATT
1 ATATTATTAAATTAATT
56454313 ATATTA-TAAA-T-ATT
1 ATATTATTAAATTAATT
56454327 ATATTA
1 ATATTA
56454333 AGAAATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 9 0.45
15 1 0.05
16 4 0.20
17 6 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATTATTAAATTAATT
Found at i:56454508 original size:14 final size:14
Alignment explanation
Indices: 56454482--56454532 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
56454472 GAAAACAAAA
56454482 GAAATAAAATAAAG
1 GAAATAAAATAAAG
*
56454496 GAAATAAAGTAAAG
1 GAAATAAAATAAAG
* * *
56454510 TAAGTTAAAATAAAA
1 GAA-ATAAAATAAAG
56454525 G-AATAAAA
1 GAAATAAAA
56454533 GAAACAAAAG
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
13 5 0.17
14 16 0.55
15 8 0.28
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.18
Consensus pattern (14 bp):
GAAATAAAATAAAG
Done.